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Tyrosine phosphorylation of RNA polymerase II CTD is associated with antisense promoter transcription and active enhancers in mammalian cells.

Descostes N, Heidemann M, Spinelli L, Schüller R, Maqbool MA, Fenouil R, Koch F, Innocenti C, Gut M, Gut I, Eick D, Andrau JC - Elife (2014)

Bottom Line: Post-translational modifications of the CTD coordinate the transcription cycle and various steps of mRNA maturation.Here we describe Tyr1 phosphorylation (Tyr1P) as a hallmark of promoter (5' associated) Pol II in mammalian cells, in contrast to what was described in yeast.Mutation of Tyr1 to phenylalanine (Y1F) prevents the formation of the hyper-phosphorylated Pol IIO form, induces degradation of Pol II to the truncated Pol IIB form, and results in a lethal phenotype.

View Article: PubMed Central - PubMed

Affiliation: Centre d'Immunologie de Marseille-Luminy, Université Aix-Marseille, Marseille, France Centre National de la Recherche Scientifique (CNRS) UMR6102, Marseille, France Inserm U631, Marseille, France Institut de Génétique Moléculaire de Montpellier (IGMM), CNRS-UMR5535, Montpellier, France.

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Ser2P average profile at genic locations and examples of Tyr1P signal at promoter locations.(A) Ser2P average profile on 1415 genes selected on mean values distribution shown in Figure 2—figure supplement 1B and represented as for Figure 2C. (B) Examples of Tyr1P (and other isoforms, short ssRNAs) at promoters of 5 coding genes. These genes show a dominance of Tyr1P (3D12) signal upstream (AS direction) relatively to downstream TSSs and as compared to Pol II and isoforms.DOI:http://dx.doi.org/10.7554/eLife.02105.011
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fig2s5: Ser2P average profile at genic locations and examples of Tyr1P signal at promoter locations.(A) Ser2P average profile on 1415 genes selected on mean values distribution shown in Figure 2—figure supplement 1B and represented as for Figure 2C. (B) Examples of Tyr1P (and other isoforms, short ssRNAs) at promoters of 5 coding genes. These genes show a dominance of Tyr1P (3D12) signal upstream (AS direction) relatively to downstream TSSs and as compared to Pol II and isoforms.DOI:http://dx.doi.org/10.7554/eLife.02105.011

Mentions: (A) Correlation plots of biological replicates (for all but H3K36me3 i.e., a technical replicate) of ChIP-seq experiments used in this study at gene locations (‘Materials and methods–Correlation of biological replicates and cross-correlation’). Spearman correlation coefficient is indicated on the top left of the plots. (B) Distribution and threshold of background-subtracted signal used for profiling of significantly bound gene (Total, i.e., whole genic regions) in Figure 2, Figure 2—figure supplement 5A, and Figure 2—figure supplement 7C. The mean values used for distribution were computed on [TSS-1000 bp:TES+2000 bp] (TSS: transcription start site; TES: transcription end site). Note that the thresholds were set to the mean of the second Gaussian of the distribution (‘Materials and methods–Gene selection and average binding profiles’). Numbers of genes selected for Pol II, Ser2P, Ser5P, Ser7P, Tyr1P 3D12, and Tyr1P 8G5 are 1521, 1536, 1543, 2382, 2652, and 2608, respectively. (C) Distribution and threshold of Pol II significantly bound promoters (TSS) as in (B). The selection is used in Figure 3, Figure 3—figure supplement 1, and Figure 3—figure supplement 2. 2044 genes were selected based on their mean values on TSS −/+ 500 bp.


Tyrosine phosphorylation of RNA polymerase II CTD is associated with antisense promoter transcription and active enhancers in mammalian cells.

Descostes N, Heidemann M, Spinelli L, Schüller R, Maqbool MA, Fenouil R, Koch F, Innocenti C, Gut M, Gut I, Eick D, Andrau JC - Elife (2014)

Ser2P average profile at genic locations and examples of Tyr1P signal at promoter locations.(A) Ser2P average profile on 1415 genes selected on mean values distribution shown in Figure 2—figure supplement 1B and represented as for Figure 2C. (B) Examples of Tyr1P (and other isoforms, short ssRNAs) at promoters of 5 coding genes. These genes show a dominance of Tyr1P (3D12) signal upstream (AS direction) relatively to downstream TSSs and as compared to Pol II and isoforms.DOI:http://dx.doi.org/10.7554/eLife.02105.011
© Copyright Policy - open-access
Related In: Results  -  Collection

License
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fig2s5: Ser2P average profile at genic locations and examples of Tyr1P signal at promoter locations.(A) Ser2P average profile on 1415 genes selected on mean values distribution shown in Figure 2—figure supplement 1B and represented as for Figure 2C. (B) Examples of Tyr1P (and other isoforms, short ssRNAs) at promoters of 5 coding genes. These genes show a dominance of Tyr1P (3D12) signal upstream (AS direction) relatively to downstream TSSs and as compared to Pol II and isoforms.DOI:http://dx.doi.org/10.7554/eLife.02105.011
Mentions: (A) Correlation plots of biological replicates (for all but H3K36me3 i.e., a technical replicate) of ChIP-seq experiments used in this study at gene locations (‘Materials and methods–Correlation of biological replicates and cross-correlation’). Spearman correlation coefficient is indicated on the top left of the plots. (B) Distribution and threshold of background-subtracted signal used for profiling of significantly bound gene (Total, i.e., whole genic regions) in Figure 2, Figure 2—figure supplement 5A, and Figure 2—figure supplement 7C. The mean values used for distribution were computed on [TSS-1000 bp:TES+2000 bp] (TSS: transcription start site; TES: transcription end site). Note that the thresholds were set to the mean of the second Gaussian of the distribution (‘Materials and methods–Gene selection and average binding profiles’). Numbers of genes selected for Pol II, Ser2P, Ser5P, Ser7P, Tyr1P 3D12, and Tyr1P 8G5 are 1521, 1536, 1543, 2382, 2652, and 2608, respectively. (C) Distribution and threshold of Pol II significantly bound promoters (TSS) as in (B). The selection is used in Figure 3, Figure 3—figure supplement 1, and Figure 3—figure supplement 2. 2044 genes were selected based on their mean values on TSS −/+ 500 bp.

Bottom Line: Post-translational modifications of the CTD coordinate the transcription cycle and various steps of mRNA maturation.Here we describe Tyr1 phosphorylation (Tyr1P) as a hallmark of promoter (5' associated) Pol II in mammalian cells, in contrast to what was described in yeast.Mutation of Tyr1 to phenylalanine (Y1F) prevents the formation of the hyper-phosphorylated Pol IIO form, induces degradation of Pol II to the truncated Pol IIB form, and results in a lethal phenotype.

View Article: PubMed Central - PubMed

Affiliation: Centre d'Immunologie de Marseille-Luminy, Université Aix-Marseille, Marseille, France Centre National de la Recherche Scientifique (CNRS) UMR6102, Marseille, France Inserm U631, Marseille, France Institut de Génétique Moléculaire de Montpellier (IGMM), CNRS-UMR5535, Montpellier, France.

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